colSums2 {DelayedMatrixStats}R Documentation

Calculates the sum for each row (column) in a matrix

Description

Calculates the sum for each row (column) in a matrix.

Usage

colSums2(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...)

rowSums2(x, rows = NULL, cols = NULL, na.rm = FALSE, dim. = dim(x), ...)

## S4 method for signature 'DelayedMatrix'
colSums2(x, rows = NULL, cols = NULL,
  na.rm = FALSE, dim. = dim(x), force_block_processing = FALSE, ...)

## S4 method for signature 'Matrix'
colSums2(x, rows = NULL, cols = NULL, na.rm = FALSE,
  dim. = dim(x), ...)

## S4 method for signature 'SolidRleArraySeed'
colSums2(x, rows = NULL, cols = NULL,
  na.rm = FALSE, dim. = dim(x), ...)

## S4 method for signature 'DelayedMatrix'
rowSums2(x, rows = NULL, cols = NULL,
  na.rm = FALSE, dim. = dim(x), force_block_processing = FALSE, ...)

## S4 method for signature 'Matrix'
rowSums2(x, rows = NULL, cols = NULL, na.rm = FALSE,
  dim. = dim(x), ...)

Arguments

x

A NxK DelayedMatrix.

rows

A vector indicating subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.

cols

A vector indicating subset of rows (and/or columns) to operate over. If NULL, no subsetting is done.

na.rm

If TRUE, NAs are excluded first, otherwise not.

dim.

An integer vector of length two specifying the dimension of x, also when not a matrix.

...

Additional arguments passed to specific methods.

force_block_processing

FALSE (the default) means that a seed-aware, optimised method is used (if available). This can be overridden to use the general block-processing strategy by setting this to TRUE (typically not advised). The block-processing strategy loads one or more (depending on getOption("DelayedArray.block.size")) columns (colFoo()) or rows (rowFoo()) into memory as an ordinary base::array.

Details

The implementation of rowSums2() and colSums2() is optimized for both speed and memory.

Value

Returns a numeric vector of length N (K).

Examples

# A DelayedMatrix with a 'matrix' seed
dm_matrix <- DelayedArray(matrix(c(rep(1L, 5),
                                   as.integer((0:4) ^ 2),
                                   seq(-5L, -1L, 1L)),
                                 ncol = 3))
# A DelayedMatrix with a 'Matrix' seed
dm_Matrix <- DelayedArray(Matrix::Matrix(c(rep(1L, 5),
                                           as.integer((0:4) ^ 2),
                                           seq(-5L, -1L, 1L)),
                                         ncol = 3))

colSums2(dm_matrix)

# NOTE: Temporarily use verbose output to demonstrate which method is
#       which method is being used
options(DelayedMatrixStats.verbose = TRUE)
# By default, this uses a seed-aware method for a DelayedMatrix with a
# 'SolidRleArraySeed' seed
rowSums2(dm_Matrix)
# Alternatively, can use the block-processing strategy
rowSums2(dm_Matrix, force_block_processing = TRUE)
options(DelayedMatrixStats.verbose = FALSE)
[Package DelayedMatrixStats version 1.2.0 Index]